CN116472277A

CN116472277A - AAV8 affinity agents

Info

Publication number: CN116472277A
Application number: CN202180068567.0A
Authority: CN
Inventors: S·巴塔查里亚; B·科伊尔; S·瓦伦蒂尼; K·卡恩斯; T·斯坎龙; W·韦尔伯恩; W·克特
Original assignee: Everbright LLC
Current assignee: Everbright LLC
Priority date: 2020-10-13
Filing date: 2021-10-13
Publication date: 2023-07-21
Also published as: JP2023545375A; EP4228779A1; KR20230113286A; US20230391829A1; WO2022081775A1

Abstract

Provided herein are affinity ligands that specifically interact with AAV8 capsids and/or AAV8 variant capsids, affinity agents comprising the affinity ligands, and methods for their use in binding, isolating and/or purifying AAV8 and variants thereof.

Description

AAV8 affinity agents

Cross Reference to Related Applications

The present application claims priority from U.S. provisional application No. 63/091,207, filed on even 13, 10/2020, the entire contents of which are incorporated herein by reference.

Technical Field

The present disclosure relates to the field of chromatography, and more particularly to novel affinity ligands and affinity agents suitable for isolating adeno-associated virus (AAV). Thus, the present disclosure encompasses the affinity ligand itself, chromatographic separation matrices (affinity agents) comprising the affinity ligand according to the present disclosure, and methods of AAV isolation, in particular AAV serotype 8 (AAV 8) isolation, wherein the ligand according to the present disclosure is used.

Background

The purity of biologically produced therapeutic agents is closely reviewed and regulated by authorities to ensure safety and effectiveness. Therefore, there is a need for efficient purification of biologically produced therapeutic agents to high purity.

In order to support the clinical efforts of advanced therapeutic drug products (ATMP), there is a need for compositions and methods for the efficient purification of ATMP from recombinant sources. Affinity purification is a means of isolating and/or obtaining the desired protein purity by several steps or by a single step. However, the development of separation matrices comprising affinity ligands bound to a solid support can be a resource intensive and time consuming task, and thus there are affinity separation matrices for very few proteins. In the absence of an affinity separation matrix, purification typically involves inefficient processes, such as multi-column processes.

Adeno-associated virus (AAV) is a member of the parvoviral family, a small non-enveloped virus. AAV particles comprise an AAV capsid consisting of 60 capsid protein subunits VP1, VP2 and VP3, comprising a single-stranded DNA genome of about 4.7 kilobases (kb). These VP1, VP2 and VP3 proteins are present in a prediction ratio of about 1:1:10, and are arranged symmetrically in icosahedron. A single particle encapsulates only one strand of DNA molecule, but this may be either a positive or negative strand, both of which are infectious. Unlike most viruses, AAV is naturally nonpathogenic, poorly immunogenic and has a broad range of tropisms. Many AAV serotypes have been identified as having variable tropism. The tissue specificity of AAV is determined by the viral capsid serotype. This specificity allows the targeting of genes of interest to certain tissues and cells. The non-pathogenic, broad infectious host range (including non-dividing cells) and integrated nature makes AAV serotypes (such as AAV 8) an attractive vehicle.

Recombinant adeno-associated virus (rAAV) is one of the most studied viral vectors for delivering human gene therapy. Recombinant AAV lacks two essential genes for viral integration and replication. Thus, rAAV remains predominantly episomal and can last long in non-dividing cells. Because of these characteristics, and the ability to target specific tissue types, recombinant AAV has become one of the major viral vectors for research and gene therapy applications. AAV serotypes exhibit a variety of cell tropisms and interactions with cellular receptors to allow entry into cells and delivery of genetic material into the nucleus for expression. Manufacture of rAAV is both difficult and expensive. Cell culture productivity is low and can usually only reach 10 per liter ¹³ -10 ¹⁵ Each viral capsid corresponds to about 0.1-10mg/L. Purification is accomplished primarily through the use of affinity chromatography. Currently, only four affinity resins are available for AAV purification, POROS ^TM CaptureSelect ^TM AAV9、POROS ^TM CaptureSelect ^TM AAVX、POROS ^TM CaptureSelect ^TM AAV8 and AVB Sepharose. These resins have two major drawbacks, namely the inability to clean with sodium hydroxide and the ability to reuse only a few cycles. This increases resin consumption and results in high costs for the resin for purification applications. Thus, there is a need for affinity agents with high specificity for AAV8 and AAV8 variants that are alkali stable and can support production and purification of AAV8 and AAV8 variants.

Disclosure of Invention

Described herein are affinity ligands and affinity agents that bind AAV8 and are useful for the isolation and/or affinity purification of AAV8 capsids and/or AAV8 variant capsids.

In one aspect, the present disclosure provides an affinity ligand that specifically binds to an AAV8 capsid or a variant capsid of AAV8, the affinity ligand comprising an amino acid sequence represented by the formula, from N-terminus to C-terminus,

[A]-X ₁ QRRX ₂ FIX ₃ X ₄ LRX ₅ DPX ₆ X ₇ SX ₈ X ₉ LLX ₁₀ X ₁₁ AX ₁₂ X ₁₃ X ₁₄ X ₁₅ X ₁₆ X ₁₇ -[B](SEQ ID NO：1)

wherein the method comprises the steps of

(a) [ A ] comprises a first alpha-helix forming peptide domain;

(b)X ₁ a, R, N, S, D, L, Q or I, preferably R;

(c)X ₂ g, H, P or S, preferably S;

(d)X ₃ is A or Y, preferably Y;

(e)X ₄ is R or S, preferably R;

(f)X ₅ e, H or Q, preferably Q;

(g)X ₆ Is E or S, preferably S;

(h)X ₇ f, V or Y, preferably F;

(i)X ₈ a, E or R, preferably a;

(j)X ₉ h, I or N, preferably H;

(k)X ₁₀ a, E or R, preferably a;

(1)X ₁₁ is D or E, preferably D;

(m)X ₁₂ is K or R, preferably K;

(n)X ₁₃ q, T or Y, preferably Y;

(o)X ₁₄ d, L or R, preferably R;

(p)X _1s is A or N, preferably N;

(q)X ₁₆ d, L or R, preferably R;

(r)X ₁₇ a, D, E, F, G, I, K, L, P, Q, R, S, T or Y, preferablyI；

(s)[B]Comprises an amino acid sequence QAPX ₁₈ (SEQ ID NO: 2) or QAPX ₁₈ Peptide of VD (SEQ ID NO: 3), wherein X ₁₈ Is A, K or R.

In certain embodiments, [ A ]]Comprising a peptide having the amino acid sequence VDAKFDKELEEARAEIERLPNLTE (SEQ ID NO: 4) or VDAKFDKELEEIRAEIERLPNLTE (SEQ ID NO: 5). In certain embodiments, in the above formula [ A ]]Is methionine (M) or MAQGT (SEQ ID NO: 6). In certain embodiments, the above formula [ B ]]Has the amino acid sequence QAPKVD (SEQ ID NO: 7) or QAPRVD (SEQ ID NO: 8). In other embodiments, [ B ]]Comprises a polypeptide having the amino acid sequence QAPX ₁₈ -[C]Peptide of (SEQ ID NO: 9), X ₁₈ A, K or R, and wherein [ C]Is a peptide domain selected from the group consisting of:

(a)VDGQAGQGGGSGLNDIFEAQKIEWHEHHHHHH(SEQ ID NO：10)，

(b)GQAGQGGGSGLNDIFESEQ ID NO：2AQKIEWHEHHHHHH(SEQ ID NO：11)，

(c) VDGLNDIFEAQKIEWHEHHHHHH (SEQ ID NO: 12) and

(d)GLNDIFEAQKIEWHEHHHHHH(SEQ ID NO：13)。

in certain embodiments, the affinity ligand further comprises a C-terminal lysine or cysteine.

In some embodiments, the affinity ligand comprises the sequence SEQ ID NO: 14-93. In other embodiments, the affinity ligand has the sequence SEQ ID NO:14 or SEQ ID NO:53. in some embodiments, the affinity ligand has the amino acid sequence of SEQ ID NO:54, while in other embodiments, the affinity ligand has the amino acid sequence of SEQ ID NO:93.

in certain embodiments, the affinity ligand comprises at least one heterologous moiety operably linked to the affinity ligand to form a conjugate. In certain embodiments, the heterologous moiety is one or more small molecule diagnostic or therapeutic agents; DNA, RNA, or hybrid DNA-RNA molecules; a trackable marker; a radioactive agent; an antibody; a single chain variable domain; or immunoglobulin fragments.

In another aspect, a multimer is provided that comprises a plurality of affinity ligands according to any of the aspects and embodiments herein. The multimer may be a dimer, trimer, tetramer, pentamer, hexamer, heptamer, octamer or nonamer.

In another aspect, a nucleic acid or vector is provided that encodes an affinity ligand or multimer of any of the aspects and embodiments herein.

In another aspect, an expression system is provided comprising any one of the nucleic acids or vectors of the present disclosure.

In yet another aspect, a separation matrix is provided comprising at least one affinity ligand or at least one multimer of any of the aspects and embodiments herein. In certain embodiments, the separation matrix comprises a plurality of affinity ligands or multimers of any of the aspects and embodiments herein coupled to a solid support. In some embodiments, the affinity ligand or multimer of the affinity matrix is coupled to the solid support via a urethane linkage. In certain embodiments of this aspect, the solid support is a chromatographic resin or matrix. In certain embodiments, the solid support is a cross-linked agarose matrix.

In another aspect, a method of isolating an adeno-associated virus subtype 8 (AAV 8) particle or capsid is provided, comprising contacting the AAV8 particle or capsid with the separation matrix of the present disclosure. In certain embodiments, the method comprises the steps of: (a) contacting a liquid sample comprising AAV8 particles or capsids with a separation matrix, (b) washing the separation matrix with a wash solution, (c) eluting AAV8 particles or capsids from the separation matrix with an elution solution, and (d) washing the separation matrix with a wash solution. In certain embodiments of this aspect, the cleaning solution comprises 0.1-0.5M NaOH. In some embodiments of this aspect, steps (a) - (d) are repeated at least ten times.

Drawings

FIG. 1 shows an example sensorgram of an example affinity agent.

Fig. 2 shows exemplary stability data for certain affinity agents of the present disclosure in the presence of 0.5M NaOH.

FIG. 3 shows SDS-PAGE gels of viral particles purified using certain provided affinity agents. The eluted (E) and stripped (S) fractions were loaded onto the gel. Reference standard (std) preparation including AAV capsids. Shows a polypeptide having the amino acid sequence SEQ ID NO: 53.

Fig. 4 shows the residence time versus the number of amino acids comprising SEQ ID NO:53 to bind to the AAV8 capsid.

Detailed Description

Definition of the definition

For easier understanding of the present disclosure, certain terms are defined below. Unless defined otherwise herein, technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this disclosure pertains.

Units, prefixes, and symbols are expressed in terms of their Syst20 (SI) acceptability. Numerical ranges include the numbers defining the ranges. Unless otherwise specified, amino acid sequences are written from left to right in the amino to carboxyl direction. The headings provided herein are not limitations of the various aspects or implementations of the disclosure which can be had by reference to the specification as a whole. Accordingly, the following directly defined terms are defined in more detail by referring to the specification in its entirety.

It is noted that the term "one or more" entities refers to one or more of the entities; for example, "affinity ligand" is understood to mean one or more affinity ligands. Thus, the terms "one or more", "one or more" and "at least one" are used interchangeably herein.

About or about: as used herein, the term "about" or "approximately" when applied to one or more values of interest refers to a value that is similar to the stated reference value. In certain embodiments, unless stated otherwise or otherwise apparent from the text (except where such numbers would exceed 100% of the possible values), the term "about" or "about" refers to a range of values that fall within either direction (greater than or less than) than 25%, 20%, 19%, 18%, 17%, 16%, 15%, 14%, 13%, 12%, 11%, 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1% or less of the stated reference value.

Biological activity: as used herein, the term "bioactive" refers to the characteristic of any agent that is active in a biological system, particularly in an organism. For example, an agent that has a biological or physiological effect on an organism when administered to the organism is considered to be biologically active.

Variants and mutants: the term "variant" is generally defined in the scientific literature and is used herein to refer to organisms that differ in some way from a recognized standard in inheritance, and "variant" may also be used to describe non-genetic phenotypic differences (King and Stansfield,2002,A dictionary of genetics, 6 th edition, new York, oxford University Press.

The term "mutation" is defined in most dictionaries and is used herein to refer to the process by which a heritable change is introduced into the genetic structure (King and Stansfield, 2002), thereby producing a "mutant". In the scientific and non-scientific literature, the term "variant" is increasingly used instead of the term "mutation". The terms are used interchangeably herein.

Conservative and non-conservative substitutions: a "conservative" amino acid substitution is a substitution in which one amino acid residue is replaced with another amino acid residue having a similar side chain. Amino acid residue families having similar side chains have been defined in the art, including basic side chains (e.g., lysine (K), arginine (R), histidine (H)); acidic side chains (e.g., aspartic acid (D), glutamic acid (E)); uncharged polar side chains (e.g., glycine (G); asparagine (N), glutamine (Q), serine (S), threonine (T), tyrosine (Y), cysteine (C)); non-polar side chains (e.g., alanine (A), valine (V), leucine (L), isoleucine (I), proline (P), phenylalanine (F), methionine (M), tryptophan (W), beta-branched side chains (e.g., threonine (T), valine (V), isoleucine (I)). And aromatic side chains (e.g., tyrosine (Y), phenylalanine (F), tryptophan (W), histidine (H)). For example, substitution of tyrosine with phenylalanine is a conservative substitution in some embodiments, conservative amino acid substitutions in the ligand sequence confer or improve specific binding of the ligand to the target of interest. In some embodiments, conservative amino acid substitutions in the ligand sequence do not reduce or eliminate specific binding of the ligand to the target of interest. In some embodiments, conservative amino acid substitutions do not significantly affect specific binding of the ligand to the target of interest. Methods of identifying, altering or maintaining selective binding affinity are known in the art (see, e.g., brmell, biochem.32: biochem. 7 (1993-1187)), amino acid substitutions in the ligand sequence confer or improve specific binding of the ligand to the target of interest (1997; amino acid substitutions in 17; protein in 1997; well-87 (1997) are) in some embodiments, amino acid substitutions in 17-879-well known in the art, non-conservative amino acid substitutions in the ligand sequence do not reduce or eliminate binding of the ligand to the target of interest. In some embodiments, non-conservative amino acid substitutions do not significantly affect the specific binding of the ligand to the target of interest.

Affinity chromatography: as used herein, the term "affinity chromatography" refers to a specific chromatographic mode in which an affinity ligand interacts with a target via biological affinity in a "lock-key" manner. Examples of interactions useful in affinity chromatography are e.g. enzyme-substrate interactions, biotin-avidin interactions, antibody-antigen interactions, etc.

Affinity ligands and ligands: the terms "affinity ligand" and "ligand" are used interchangeably herein. These terms are used herein to refer to molecules capable of reversibly binding with high affinity to a moiety, such as a polypeptide or protein, specific for it.

Protein-based ligands: the term "protein-based ligand" as used herein refers to a ligand comprising a peptide or protein or a portion of a peptide or protein that reversibly binds to a target polypeptide or protein. It should be understood that the "ligands" of the present disclosure are protein-based ligands.

Affinity agent: as used herein, the term "affinity agent" refers to a solid support or matrix to which biospecific affinity ligands are covalently attached. Typically, the solid support or matrix is insoluble in the system for purifying the target molecule. The terms "affinity agent" and "affinity separation matrix" and "separation matrix" are used interchangeably herein.

And (3) joint: as used herein, "linker" refers to a peptide or other chemical linkage that serves to link other independent functional domains. In some embodiments, the linker is located between the ligand and another polypeptide component containing an additional independent functional or structural domain. In some embodiments, the linker is a peptide or other chemical bond between the ligand and the surface.

Naturally occurring: the term "naturally occurring" when used in connection with biological materials such as nucleic acid molecules, polypeptides and host cells refers to those found in nature and not modified by humans. Conversely, when used in connection with biological materials, "non-natural" or "synthetic" refers to those materials that are not found in nature and/or have been modified by humans.

"unnatural amino acid", "amino acid analog" and "nonstandard amino acid residue" are used interchangeably herein. Unnatural amino acids that can be substituted in the ligands provided herein are known in the art. In some embodiments, the unnatural amino acid is a proline-substituted 4-hydroxyproline; 5-hydroxylysine that can be substituted for lysine; 3-methylhistidine, which may be substituted for histidine; homoserine which can replace serine; and ornithine substituted for lysine. Other examples of unnatural amino acids that can be substituted in a polypeptide ligand include, but are not limited to, molecules such as: d-isomers of common amino acids, 2, 4-diaminobutyric acid, alpha-aminoisobutyric acid, A-aminobutyric acid, abu, 2-aminobutyric acid, gamma-Abu, epsilon-Ahx, 6-aminocaproic acid, aib, 2-aminoisobutyric acid, 3-aminopropionic acid, ornithine, norleucine, norvaline, hydroxyproline, sarcosine, citrulline, homocysteine, t-butylglycine, t-butylalanine, phenylglycine, cyclohexylalanine, beta-alanine, lanthionine, dehydroalanine, gamma-aminobutyric acid, selenocysteine and pyrrolysine fluoroamino acids, designer amino acids such as beta-methylamino acid, C alpha-methylamino acid and N alpha-methylamino acid.

"Polynucleotide" and "nucleic acid molecule": as used interchangeably herein, polynucleotide and nucleic acid molecules refer to polymeric forms of nucleotides of any length (ribonucleotides or deoxyribonucleotides). These terms include, but are not limited to DNA, RNA, cDNA (complementary DNA), mRNA (messenger RNA), rRNA (ribosomal RNA), shRNA (small hairpin RNA), snRNA (microrna), snoRNA (short nucleolar RNA), miRNA (microrna), genomic DNA, synthetic RNA, and/or tRNA (transfer RNA).

Operatively connected to: as used herein, the term "operably connected" means the possibility that two or more components are arranged such that they function properly and that at least one component is permitted to mediate a function imposed on at least one other component. Whether attached directly or indirectly, two molecules are "operably linked".

Peptide tag: the term "peptide tag" as used herein refers to a peptide sequence that is part of or attached (e.g., by genetic engineering) to another protein to provide functionality to the fusion produced thereby. Peptide tags are generally relatively short compared to the proteins they are fused to. In some embodiments, the peptide tag is four or more amino acids in length, such as 5, 6, 7, 8, 9, 10, 15, 20, or 25 or more amino acids. In some embodiments, the ligand is a protein containing a peptide tag. Many peptide tags having the uses as provided herein are known in the art. Examples of peptide tags that may be components of the ligand fusion protein or targets bound by the ligand (e.g., ligand fusion protein) include, but are not limited to, HA (hemagglutinin), c-Myc, herpes simplex virus glycoprotein D (gD), T7, GST, GFP, MBP, strep tags, his tags, myc tags, TAP tags, and FLAG tags (Eastman Kodak, rochester, n.y.). Also, antibodies directed against the tag epitope allow detection and localization of the fusion protein in, for example, affinity purification, western blotting, ELISA assays, and cell immunostaining.

Polypeptide: the term "polypeptide" as used herein refers to a continuous chain of amino acids linked together via peptide bonds. The term is used to refer to chains of amino acids of any length, but one of ordinary skill in the art will appreciate that the term is not limited to long chains and may refer to a smallest chain comprising two amino acids linked together via a peptide bond. The polypeptides may be processed and/or modified as known to those skilled in the art.

Protein: the term "protein" as used herein refers to one or more polypeptides that act as discrete units. The terms "polypeptide" and "protein" are used interchangeably if a single polypeptide is a discrete functional unit and does not require permanent or temporary physical association with other polypeptides to form the discrete functional unit. If a discrete functional unit consists of more than one polypeptide physically associated with each other, the term "protein" refers to a plurality of polypeptides that are physically coupled and function together as a discrete unit.

Specific binding: as used herein, the term "specifically binds" or "has a selective affinity" with respect to a ligand means that the ligand reacts or associates with a particular epitope, protein, or target molecule more frequently, more rapidly, for a longer duration, with greater affinity, or a combination thereof than with an alternative substance (including an unrelated protein). Due to sequence identity between homologous proteins in different species, specific binding may include binding agents that recognize proteins or targets in more than one species, e.g., bispecific or trispecific. Also, due to homology within certain regions of polypeptide sequences of different proteins, specific binding may include binding agents that recognize more than one protein or target. It will be appreciated that in certain embodiments, a binding agent that specifically binds to a first target may or may not specifically bind to a second target. Thus, "specific binding" does not necessarily require (although it may include) exclusive binding, i.e., binding to a single target. Thus, in certain embodiments, a ligand or affinity agent may specifically bind to more than one target. In certain embodiments, multiple targets may be bound by the same binding site on the affinity agent.

Basically: as used herein, the term "substantially" refers to a qualitative condition that exhibits a feature or characteristic of interest in an overall or near-overall range or degree. It will be appreciated by those of ordinary skill in the biological arts that little, if any, biological and chemical phenomena may be accomplished and/or proceed to completion or achieve or avoid absolute results. Thus, the term "substantially" is used herein to achieve inherent completeness that is potentially lacking in many biological and chemical phenomena.

The present disclosure specifically encompasses highly purified preparations, such as, for example, adeno-associated virus (AAV) particles, more specifically AAV8 particles, using affinity agents comprising peptide ligands attached to a solid support to produce one or more targets of interest. In some embodiments, the affinity agents described herein are particularly useful for removing impurities associated with protein products as well as host cell-derived contaminants.

AAV8 affinity ligands

The ligands of the various aspects and embodiments of the disclosure are high affinity protein ligands that reversibly bind to AAV8 capsids and/or AAV8 variant capsids. Many AAV8 variants are known in the art. (e.g., AAV8 variants (Y733F, Y447F, Y447F) GeneMedi; see also Gilkes et al, site-specific modifications to AAV8 capsid yields enhanced brain transduction in the neonatal MPS IIIB mouse, gene therapy,28:447-455 (2021.) non-limiting uses of the target molecule include therapeutic and diagnostic uses.

Affinity ligands of the present disclosure have the general formula:

[A]-X ₁ QRRX ₂ FIX ₃ X ₄ LRX ₅ DPX ₆ X ₇ SX ₈ X ₉ LLX ₁₀ X ₁₁ AX12X ₁₃ X ₁₄ X ₁₅ X ₁₆ X ₁₇ -[B](SEQ ID NO: 1), wherein

[A]Comprising a first α -helix forming peptide domain; x is X ₁ A, R, N, S, D, L, Q or I, preferably R;

X ₂ g, H, P or S, preferably S; x is X ₃ Is A or Y, preferably Y; x4 is R or S, preferably R; x is X ₅ E, H or Q, preferably Q; x is X ₆ Is E or S, preferably S; x is X ₇ F, V or Y, preferably F; x is X ₈ A, E or R, preferably a; x is X ₉ H, I or N, preferably H; x is X ₁₀ A, E or R, preferably a; x is X ₁₁ Is D or E, preferably D; x is X ₁₂ Is K or R, preferably K; x is X ₁₃ Q, T or Y, preferably Y; x is X ₁₄ D, L or R, preferably R; x is X ₁₅ Is A or N, preferably N; x is X ₁₆ D, L or R, preferably R; x is X ₁₇ A, D, E, F, G, I, K, L, P, Q, R, S, T or Y, preferably I; and [ B ]]Comprises an amino acid sequence QAPX ₁₈ (SEQ ID NO: 2) or QAPX ₁₈ Peptide of VD (SEQ ID NO: 3), wherein X ₁₈ Is A, K or R.

Part [ A ] of the above formula is a peptide providing an alpha-helical structure to the N-terminus of the ligand. In some embodiments, [ A ] has the amino acid sequence VDAKFDKELEEARAEIERLPNLTE (SEQ ID NO: 4). In other embodiments, [ A ] has the amino acid sequence VDAKFDKELEEIRAEIERLPNLTE (SEQ ID NO: 5). The N-terminus of the affinity ligand (i.e., the N-terminus of [ A ]) may be methionine or may include the additional amino acid sequence MAQGT (SEQ ID NO: 6).

Moiety of formula (I) of the affinity ligand of the present disclosure [ B]There may be, for example, the amino acid sequence QAPK VD (SEQ ID NO: 7) or QAPRVD (SEQ ID NO: 8). In other embodiments, [ B ]]Having the amino acid sequence QAPX ₁₈ -[C](SEQ ID NO: 9), wherein [ C]Is a polypeptide having the amino acid sequence VDGQAGQGGGSGLNDIFEAQKIEWHEHHHHHH (SEQ ID NO: 10); GQAGQGGGSGLNDIFEAQKIEWHEHHHHHH (SEQ ID NO: 11); VDGLNDIFEAQKIEWHEHHHHHH (SEQ ID NO: 12) or GLNDIFEAQKIEWHEHHHHHH (SEQ ID NO: 13) and X ₁₈ Is A, K or R.

The affinity ligand may have the amino acid sequence SEQ ID No: 14-93. In certain embodiments, the affinity ligand has the amino acid sequence of SEQ ID NO:14, while in other embodiments, the affinity ligand has the amino acid sequence of SEQ ID NO:53. in some embodiments, the affinity ligand has the amino acid sequence of SEQ ID NO:54. in some embodiments, the affinity ligand has the amino acid sequence of SEQ ID NO:93.

in another aspect, the present disclosure provides a multimer comprising a plurality of affinity ligands (units) as defined in any of the embodiments disclosed above. The multimer may be a dimer, trimer, tetramer, pentamer, hexamer, heptamer, octamer or nonamer. The multimer may be a homomultimer in which all ligand units are the same, or the multimer may be a heteromultimer in which at least one ligand unit is different from the others. The ligands may be directly linked to each other by a peptide bond between the C-terminus and the N-terminus of the ligand. Alternatively, two or more ligand units of a multimer may be linked by a linker comprising an oligomeric or polymeric species, such as an element comprising up to 15 or 30 amino acids, such as 1-5, 1-10, or 5-10 amino acids.

In some embodiments of this aspect, the multimers of the present disclosure have the following structural formula:

[ [ A ] -core-QAPX ] nC ] (SEQ ID NO: 95),

wherein [ A ]]Is VDAKFDKELEEARAEIERLPNLTE (SEQ ID NO: 4), [ C ]]VDGLNDIFEAQKIEWHEHHHHHH (SEQ ID NO: 12), and the core is X ₁ QRRX ₂ FIX ₃ X ₄ LRX ₅ DPX ₆ X ₇ SX ₈ X ₉ LLX ₁ ₀ X ₁₁ AX ₁₂ X ₁₃ X ₁₄ X ₁₅ X ₁₆ X ₁₇ Wherein X is ₁ -X ₁₇ As defined above for the affinity ligand, X is A, K or R and n is any number between 2 and 10. (SEQ ID NO: 96). Optionally, the N-terminus of the structure is M or MAQGT (SEQ ID NO: 6).

In some embodiments, the ligands and/or multimers as disclosed above further comprise one or more coupling elements at the C-terminus or N-terminus, such as one or more cysteine residues, one or more lysine residues, or a plurality of histidine residues. In certain embodiments, the affinity ligand and/or multimer further comprises a heterologous agent operably linked to the ligand and/or multimer, such as, for example, one or more of the following: a small molecule diagnostic or therapeutic agent; DNA, RNA or hybrid DNA-RNA; a trackable marker; a radioactive agent; an antibody; a single chain variable domain; or immunoglobulin fragments.

Ligands that bind to AAV8

The identity of ligands or multimers that bind to a target, such as AAV8 and/or AAV8 variants, can be determined using known or improved assays, bioassays, and/or animal models known in the art for assessing such activity.

As used herein, terms such as "binding affinity to a target," "binding to AAV8 and/or AAV8 variants," and the like refer to properties of the ligands of the disclosure that can be directly measured, for example, by an assay of affinity constants (e.g., the amount of ligand that associates and dissociates at a given antigen concentration). There are several methods available for characterizing such molecular interactions, for example, competition analysis, equilibrium analysis and micro-thermal analysis, as well as real-time interaction analysis based on surface plasmon resonance interactions (e.g., using a BIACORE instrument). These methods are well known to those skilled in the art and are described, for example, in Neri D et al (1996) Tibtech14:465-470 and Jansson M et al (1997) J Biol Chem 272: 8189-8197.

The affinity requirements of a given ligand binding event depend on a variety of factors including, but not limited to, the composition and complexity of the binding matrix, the valency and density of the ligand and target molecule, and the functional application of the ligand. In some embodiments, the ligands of the present disclosure are present in an amount of less than or equal to 5 x 10 ^-3 M、10 ^-3 M、5×10 ^-4 M、10 ^-4 M、5×10 ^-5 M or 10 ^-5 The dissociation constant (KD) of M binds AAV8 or a variant of AAV 8. In some embodiments, the ligand is present in an amount of less than or equal to 5X 10 ^-6 M、10 ^-6 M、5×10 ^-7 M、10 ^-7 M、5×10 ^-8 M or 10 ^-8 KD of M binds to a target of interest. In some embodiments, the ligand is present in an amount of less than or equal to 5X 10 ^-9 M、10 ^-9 M、5×10 ^-10 M、10 ^-10 M、5×10 ^-11 M、10 ^-11 M、5×10 ^-12 M、10 ^-12 M、5×10 ^-13 M、10 ^-13 M、5×10 ^-14 M、10 ^-14 M、5×10 ^-15 M or 10 ^-15 KD of M binds to a target of interest. In some embodiments, the ligand produced by the methods disclosed herein has the following dissociation constants: about 10 ^-4 M to about 10 ^-5 M, about 10 ^-5 M to about 10 ^-6 M, about 10 ^-6 M to about 10 ^-7 M, about 10 ^-7 M to about 10 ^-8 M, about 10 ^-8 M to about 10 ^-9 M, about 10 ^-9 M to about 10 ^-10 M, about 10 ^-10 M to about 10 ^-11 M or about 10 ^-11 M to about 10 ^-12 M。

In some embodiments, the ligand or multimer of the present disclosure specifically binds to an AAV8 particle or plasmid, or AAV8 variant particle or plasmid, with a koff within the following ranges: 0.1 to 10 ^-7 Second-1, 10 ^-2 To 10 ^-7 Second of ^-1 Or 0.5X10 ^-2 To 10 ^-7 Second-1. In some embodiments, the ligand binds to the target of interest at an off rate (koff) less than: 5X 10 ^-2 Second of ^-1 、10 ^-2 Second of ^-1 、5×10 ^-3 Second-1 or 10 ^-3 Second of ^-1 . In some embodiments, the ligand binds to the target of interest at an off rate (koff) less than: 5X 10 ^-4 Second of ^-1 、10 ^-4 Second of ^-1 、5×10 ^-5 Second of ^-1 Or 10 ^-5 Second of ^-1 、5×10 ^-6 Second of ^-1 、10 ^-6 Second of ^-1 、5×10 ^-7 Second of ^-1 Or 10 ^-7 Second of ^-1 。

In some embodiments, the ligand or multimer specifically binds to an AAV8 particle or plasmid, or AAV8 variant particle or plasmid, with a kon within the following range: 10 ³ To 10 ⁷ M ^-1 Second of ^-1 、10 ³ To 10 ⁶ M ^-1 Second of ^-1 Or 10 ³ To 10 ⁵ M ^-1 Second of ^-1 . In some embodiments, the ligand (e.g., ligand fusion protein) binds to the target of interest at an association rate (kon) greater than: 10 ³ M ^-1 Second of ^-1 、5×10 ³ M ^-1 Second of ^-1 、10 ⁴ M ^-1 Second of ^-1 Or 5X 10 ⁴ M ^-1 Second of ^-1 . In a further embodiment, the ligand binds to the target of interest with a kon greater than: 10 ⁵ M ^-1 Second of ^-1 、5×10 ⁵ M ^-1 Second of ^-1 、10 ⁶ M ^-1 Second of ^-1 、5×10 ⁶ M ^-1 Second of ^-1 Or 10 ⁷ M ^-1 Second of ^-1 。

Joint

The terms "linker" and "spacer" are used interchangeably herein to refer to a peptide or other chemical linkage that serves to link other independent functional domains. In some embodiments, the linker is located between the ligand and another polypeptide component comprising an additional independent functional domain. Suitable linkers for coupling two or more linked ligands may generally be any linker used in the art for linking peptides, proteins or other organic molecules. In some embodiments, this linker is suitable for use in constructing proteins or polypeptides intended for pharmaceutical use.

Suitable linkers for operably linking the ligand and additional components of the ligand fusion protein in a single chain amino acid sequence include, but are not limited to, polypeptide linkers, such as glycine linkers, serine linkers, mixed glycine/serine linkers, glycine and serine rich linkers, or linkers composed primarily of polar polypeptide fragments.

In some embodiments, the linker comprises a majority of amino acids selected from the group consisting of: glycine, alanine, proline, asparagine, glutamine and lysine. In some embodiments, the linker comprises a majority of amino acids selected from the group consisting of: glycine, alanine, proline, asparagine, aspartic acid, threonine, glutamine, and lysine. In some embodiments, the ligand linker consists of a majority of amino acids that are not sterically hindered. In some embodiments, the linker comprises a majority of amino acids selected from glycine, serine, and/or alanine. In some embodiments, the linker is selected from the group consisting of poly glycine (such as (Gly) 5 and (Gly) 8), poly (Gly-Ala), and poly alanine.

The linkers can have any size or composition so long as they are capable of operably linking the ligand in a manner that allows the ligand to bind to the target of interest. In some embodiments, the linker is about 1 to 50 amino acids, about 1 to 20 amino acids, about 1 to 15 amino acids, about 1 to 10 amino acids, about 1 to 5 amino acids, about 2 to 20 amino acids, about 2 to 15 amino acids, about 2 to 10 amino acids, or about 2 to 5 amino acids. It should be clear that the length, degree of flexibility and/or other properties of the linker may affect certain properties of the ligand for the affinity agent, such as affinity, specificity or avidity for the target of interest, or one or more other target proteins of interest, or proteins not of interest (i.e. non-target proteins). In some embodiments, two or more linkers are used. In some embodiments, two or more linkers are the same. In some embodiments, two or more linkers are different.

In some embodiments, the linker is a non-peptide linker such as an alkyl linker or a PEG linker. For example, alkyl linkers such as-NH- (CH 2) s-C (0) -, where s=2-20, can be used. These alkyl linkers may also be substituted with any non-sterically hindered group, such as lower alkyl (e.g., C1C 6), lower acyl, halogen (e.g., CI, br), CN, NH2, phenyl, and the like. An exemplary non-peptide linker is a PEG linker. In some embodiments, the PEG linker has a molecular weight of about 100 to 5000kDa or about 100 to 500 kDa.

Other techniques described herein and/or known in the art may be used to evaluate the linker. In some embodiments, the linker does not alter (e.g., does not disrupt) the ability of the ligand to bind to the target molecule.

Affinity agents comprising conjugated ligands: affinity separation matrix

Ligands or multimers that promote specific binding to a target of interest can be chemically conjugated to a variety of surfaces used in chromatography, e.g., beads, resins, gels, membranes, monoliths, etc., to prepare affinity agents. The affinity agents of the present disclosure are particularly useful for AAV8 and AAV8 variant purification and manufacturing applications.

In some embodiments, the ligands of the present disclosure (e.g., ligand fusion proteins) contain at least one reactive residue. The reactive residues may be used as attachment sites for, for example, conjugates, such as chemotherapeutic drugs or diagnostic agents. Exemplary reactive amino acid residues include, for example, lysine or cysteine. The reactive residue may be added to either end of the ligand or within the ligand sequence, and/or may replace another amino acid within the ligand sequence. Suitable reactive residues (e.g., lysine, cysteine, etc.) may also be located within the sequence of the identified ligand without the need for additions or substitutions.

Attachment to solid surfaces

"solid surface," "support," or "matrix" are used interchangeably herein and refer to, but are not limited to, any column (or column material), bead, tube, microtiter plate, solid particle (e.g., agarose or sepharose), microchip (e.g., silicon, silica glass, or gold chip), or membrane of origin (synthetic (e.g., filter) or biological (e.g., liposome or vesicle)), to which a ligand or multimer of the present disclosure can be attached (i.e., coupled, linked, or adhered) directly or indirectly (e.g., through other binding partner intermediates, such as linkers), or to which the ligand or multimer can be embedded (e.g., through receptors or channels). Reagents and techniques for attaching polypeptides to solid supports are well known in the art, such as carbamate coupling. Suitable solid supports include, but are not limited to, chromatographic resins or matrices (e.g., SEPHAROSE-4 FF agarose beads), well walls or bottoms in plastic microtiter plates, silica-based biochips, polyacrylamides, agarose, silica, nitrocellulose, paper, plastics, nylon, metals, and combinations thereof. The ligands and other compositions may be attached to the support material by non-covalent association or by covalent bonding using reagents and techniques known in the art. In some embodiments, the ligand is coupled to the chromatographic material using a linker.

In one aspect, the present disclosure provides an affinity agent (affinity separation matrix) consisting of a ligand or multimer as described above coupled to an insoluble support. The support may be one or more particles, such as beads; a membrane; a filter; a capillary tube; a monolithic column; as well as any other form commonly used in chromatography. In an advantageous embodiment of the affinity separation matrix, the support consists of substantially spherical particles (also called beads). Suitable particle sizes may be in the range of 5-500 μm, such as 10-100 μm, e.g. 20-80 μm in diameter. In an alternative embodiment, the support is a membrane. In order to obtain a high adsorption capacity, the support is preferably porous, and the ligand may be coupled to the outer surface as well as to the pore surface. In an advantageous embodiment of this aspect, the support is porous.

In another aspect, the present disclosure relates to a method of preparing a chromatographic affinity agent, the method comprising providing a ligand as described above, and coupling the ligand to a support. For example, coupling may be via the nitrogen or sulfur atom of the ligand. The ligand may be coupled to the support directly or indirectly via a spacer element providing a suitable distance between the support surface and the ligand. Methods for immobilizing protein ligands to porous or non-porous surfaces are well known in the art.

Ligand production

The ligands and multimers useful in practicing several embodiments of the present disclosure can be generated using a variety of standard techniques known in the art for chemical synthesis, semisynthetic methods, and recombinant DNA methods. Methods for producing ligands and multimers as soluble agents and cell-associated proteins are also provided, either alone or as part of a multi-domain fusion protein. In some embodiments, the overall production scheme of the ligand or multimer includes obtaining a reference protein scaffold and identifying multiple residues within the scaffold for modification. According to embodiments, the reference scaffold may comprise a protein structure or other tertiary structure having one or more alpha-helical regions. Once identified, any of a number of residues may be modified, for example by substitution of one or more amino acids. In some embodiments, one or more conservative substitutions are made. In some embodiments, one or more non-conservative substitutions are made. In some embodiments, a natural amino acid (e.g., one of alanine, arginine, asparagine, aspartic acid, cysteine, glutamine, glutamic acid, glycine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, serine, threonine, tryptophan, tyrosine, or valine) is substituted into the reference scaffold at the target site. In some embodiments, the modification does not include substitution of cysteine or proline. After modification at the identified location desired for a particular embodiment, the resulting modified polypeptides (e.g., candidate ligands) may be recombinantly expressed, e.g., in a plasmid, bacteria, phage, or other vector (e.g., to increase the number of polypeptides per modification). The modified polypeptides can then be purified and screened to identify those modified polypeptides that have specific binding to a particular target of interest (e.g., AAV8 or a variant of AAV 8). The modified polypeptide may exhibit enhanced binding specificity for AAV8 or a variant of AAV8, or may exhibit little or no binding to a given target (or non-target protein) of interest, as compared to a reference scaffold. In some embodiments, depending on the target of interest, the reference scaffold may exhibit some interactions (e.g., non-specific interactions) with the target of interest, while certain modified polypeptides will exhibit at least about two-fold, at least about five-fold, at least about ten-fold, at least about 20-fold, at least about 50-fold, or at least about 100-fold (or more) increased binding specificity for the target of interest. Additional details regarding the generation, selection, and isolation of ligands are provided in more detail below.

Recombinant expression of ligands

In some embodiments, the ligand, such as a ligand fusion protein, is "recombinantly produced" (i.e., produced using recombinant DNA techniques). Exemplary recombinant methods that can be used to synthesize the ligand fusion protein include, but are not limited to, polymerase Chain Reaction (PCR) -based synthesis, concatamerization, seamless cloning, and Recursive Directional Ligation (RDL) (see, e.g., meyer et al, biomacromol ecules 3:357-367 (2002), kurihara et al, biotechnol. Lett.27:665-670 (2005), haider et al, mol. Pharm.2:139-150 (2005), and McMillan et al, macromolecules 32 (11): 3643-3646 (1999).

In another aspect, there is also provided a nucleic acid comprising a polynucleotide sequence encoding a ligand or multimer according to the embodiments disclosed above. Thus, the present disclosure encompasses all forms of the nucleic acid sequences of the invention, such as RNA and DNA encoding polypeptides (ligands) or multimers. The present disclosure provides vectors, such as plasmids, that contain, in addition to the coding sequence, the signal sequences required for expression of a polypeptide or multimer according to the present disclosure. Such polynucleotides optionally further comprise one or more expression control elements. For example, a polynucleotide may comprise one or more promoters or transcription enhancers, ribosome binding sites, transcription termination signals and polyadenylation signals as expression control elements. The polynucleotide may be inserted into any suitable vector, which may be contained within any suitable host cell for expression. In one embodiment, the vector comprises a nucleic acid encoding a multimer according to the present disclosure, wherein the individual nucleic acids encoding each unit may have homologous or heterologous DNA sequences.

Expression of the nucleic acids encoding the ligands and multimers is typically achieved by operably linking the nucleic acids encoding the ligands to a promoter in an expression vector. Typical expression vectors contain transcriptional and translational terminators, initiation sequences, and promoters useful for regulating the expression of the desired nucleic acid sequence. Exemplary promoters useful for expression in E.coli include, for example, the T7 promoter.

Methods known in the art can be used to construct expression vectors containing ligand-encoding nucleic acid sequences and appropriate transcriptional/translational control signals. These methods include, but are not limited to, recombinant DNA techniques in vitro, synthetic techniques, and recombinant/gene recombination in vivo. Expression of the polynucleotide may be carried out in any suitable expression host known in the art, including but not limited to bacterial cells, yeast cells, insect cells, plant cells, or mammalian cells. In some embodiments, the nucleic acid sequence encoding the ligand is operably linked to a suitable promoter sequence such that the nucleic acid sequence is transcribed and/or translated into the ligand in the host.

A variety of host expression vector systems may be utilized to express the nucleic acid encoding the ligand. Vectors containing nucleic acids encoding a ligand (e.g., a single ligand subunit or ligand fusion) or a portion or fragment thereof include plasmid vectors, single-and double-stranded phage vectors, and single-and double-stranded RNA or DNA viral vectors. Phage and viral vectors can also be introduced into host cells in packaged or packaged virus form using known infection and transduction techniques. Furthermore, the viral vector may be replication competent or replication defective. Alternatively, cell-free translation systems may also be used to produce proteins using RNA derived from DNA expression constructs (see, e.g., WO86/05807 and WO89/01036; and U.S. Pat. No. 5,122,464).

In general, any type of cell or cultured cell line can be used to express the ligands or multimers provided herein. In some embodiments, the background cell line used to generate the engineered host cell is a phage, bacterial cell, yeast cell, or mammalian cell. A variety of host expression vector systems may be used to express the coding sequence of the ligand fusion protein. Mammalian cells can be used as host cell systems transfected with recombinant plasmid DNA or cosmid DNA expression vectors containing the target coding sequences of interest and the fusion polypeptide coding sequences. The cells may be primary isolates from organisms, cultures or cell lines having transformed or transgenic properties.

Suitable host cells include, but are not limited to, microorganisms, such as bacteria (e.g., E.coli, B.subtilis) transformed with recombinant phage DNA, plasmid DNA, or cosmid DNA expression vectors containing ligand-encoding sequences; yeasts transformed with recombinant yeast expression vectors containing ligand coding sequences (e.g., saccharomyces, pichia (Pichia)); insect cell systems infected with recombinant viral expression vectors (e.g., baculovirus) containing ligand coding sequences; plant cell systems infected with recombinant viral expression vectors (e.g., cauliflower mosaic virus, caMV; tobacco mosaic virus, TMV) or transformed with recombinant plasmid expression vectors (e.g., ti plasmid) containing ligand coding sequences.

Prokaryotes that can be used as host cells in the production of ligands include gram-negative or gram-positive organisms such as E.coli and B.subtilis. Expression vectors for prokaryotic host cells typically contain one or more phenotypic selection marker genes (e.g., genes encoding proteins that confer antibiotic resistance or provide autotrophic requirements). Examples of useful prokaryotic host expression vectors include pKK223-3 (Pharmacia, uppsala, sweden), pGEMl (Promega, wis., USA), pET (Novagen, wis., USA) and pRSET (Invitrogen, calif., USA) series vectors (see, e.g., studier, J.mol. Biol.219:37 (1991) and Schoepfer, gene 124:83 (1993)). Exemplary promoter sequences frequently used in prokaryotic host cell expression vectors include T7 (Rosenberg et al, gene 56:125-135 (1987)), beta-lactamase (penicillinase), lactose promoter systems (Chang et al, nature 275:615 (1978)); and Goeddel et al, nature 281:544 (1979)), tryptophan (trp) promoter system (Goeddel et al, nucleic acids res.8:4057, (1980)) and the tac promoter (Sambrook et al, 1990,Molecular Cloning,A Laboratory Manual, 2 nd edition, cold Spring Harbor Laboratory, cold Spring Harbor, n.y.).

In some embodiments, eukaryotic host cell systems are used, including yeast cells transformed with recombinant yeast expression vectors containing ligand-encoding sequences. Exemplary yeasts useful for producing the compositions of the present disclosure include yeasts from Saccharomyces, pichia, actinomyces, and Kluyveromyces (Kluyveromyces). Yeast vectors typically contain an origin of replication sequence, an Autonomously Replicating Sequence (ARS), a promoter region, a polyadenylation sequence, a transcription termination sequence and a selectable marker gene from a 2mu yeast plasmid. Examples of promoter sequences in yeast expression constructs include promoters from: metallothionein, 3-phosphoglycerate kinase (Hitzeman, J.biol. Chem.255:2073 (1980)) and other glycolytic enzymes such as enolase, glyceraldehyde-3-phosphate dehydrogenase, hexokinase, pyruvate decarboxylase, phosphofructokinase, glucose-6-phosphate isomerase, 3-phosphoglycerate mutase, pyruvate kinase, triose phosphate isomerase, phosphoglucose isomerase and glucokinase. Other suitable vectors and promoters for yeast expression and yeast transformation protocols are known in the art. See, e.g., fleer, gene 107:285-195 (1991) and Hinnen, PNAS 75:1929 (1978).

Insect and plant host cell culture systems may also be used to produce the compositions of the present disclosure. Such host cell systems include, for example, insect cell systems infected with recombinant viral expression vectors (e.g., baculovirus) containing ligand-encoding sequences; plant cell systems infected with recombinant viral expression vectors (e.g., cauliflower mosaic virus, caMV; tobacco mosaic virus, TMV) or transformed with recombinant plasmid expression vectors containing ligand coding sequences (e.g., ti plasmid), including but not limited to U.S. Pat. No. 6,815,184; U.S. publication nos. 60/365,769 and 60/368,047; and expression systems as taught in WO2004/057002, WO2004/024927 and WO 2003/078614.

In some embodiments, host cell systems, including animal cell systems infected with recombinant viral expression vectors (e.g., adenovirus, retrovirus, adeno-associated virus, herpes virus, lentivirus), including cell lines engineered to contain multiple copies of DNA encoding stably amplified (CHO/dhfr) or unstably amplified ligands in double minichromosomes (e.g., murine cell lines) may be used. In some embodiments, the vector comprising the polynucleotide encoding the ligand is polycistronic. Exemplary mammalian cells that can be used to produce these compositions include 293 cells (e.g., 293T and 293F), CHO cells, BHK cells, NS0 cells, SP2/0 cells, YO myeloma cells, P3X63 mouse myeloma cells, PER cells, per.c6 (Crucell, netherlands) cells VERY, hela cells, COS cells, MDCK cells, 3T3 cells, W138 cells, BT483 cells, hs578T cells, HTB2 cells, BT20 cells, T47D cells, CRL7O30 cells, hsS Bst cells, hybridoma cells, and other mammalian cells. Other exemplary mammalian host cells that can be used to practice embodiments of the present disclosure include, but are not limited to, T cells. Exemplary expression systems and selection methods are known in the art and include those described in the following references and references cited therein: borth et al, biotechnol. Bioen.71 (4): 266-73 (2000); werner et al, arzneimittelforschung/Drug Res.48 (8): 870-80 (1998); andersen et al, curr.op.biotechnol.13:117-123 (2002); chadd et al, curr.op, biotechnol.12:188-194 (2001), giddings, curr.Op. Biotechnol.12:450-454 (2001). Other examples of expression systems and selection methods are described in Logan et al, PNAS 81:355-359 (1984); birtner et al Methods enzymol.153:51-544 (1987)). The transcriptional and translational control sequences of mammalian host cell expression vectors are typically derived from the viral genome. Promoter sequences and enhancer sequences commonly used in mammalian expression vectors include sequences derived from polyoma virus, adenovirus 2, simian virus 40 (SV 40) and human Cytomegalovirus (CMV). Exemplary commercially available expression vectors for mammalian host cells include pCEP4 (Invitrogen) and pcDNA3 (Invitrogen).

Physical methods for introducing nucleic acids into host cells (e.g., mammalian host cells) include calcium phosphate precipitation, lipofection, particle bombardment, microinjection, electroporation, and the like. Methods for producing cells comprising vectors and/or exogenous nucleic acids are well known in the art. See, e.g., sambrook et al (2001,Molecular Cloning:A Laboratory Manual,Cold Spring Harbor Laboratory,New York).

Biological methods for introducing a polynucleotide of interest into a host cell include the use of DNA and RNA vectors. Viral vectors, and in particular retroviral vectors, have become the most widely used method of inserting genes into mammalian (e.g., human) cells. Other viral vectors may be derived from lentiviruses, poxviruses, herpes simplex virus I, adenoviruses, adeno-associated viruses, and the like. See, for example, U.S. patent nos. 5,350,674 and 5,585,362.

Methods for introducing DNA and RNA polynucleotides of interest into a host cell include electroporation of the cell, wherein an electric field is applied to the cell to increase the permeability of the cell membrane, thereby allowing chemicals, drugs, or polynucleotides to be introduced into the cell. Electroporation may be used to introduce ligands containing DNA or RNA constructs into mammalian cells or prokaryotic cells.

In some embodiments, electroporation of the cells results in expression of the ligand-CAR on the surface of T cells, NK cells, NKT cells. This isSeed expression may be transient or stable throughout the life cycle of the cell. Electroporation can be accomplished by methods known in the art, including MaxCyteAnd->Transfection System (MaxCyte, gaithersburg, md., USA).

Chemical means for introducing polynucleotides into host cells include colloidal dispersion systems such as macromolecular complexes, nanocapsules, microspheres, beads and lipid-based systems, including oil-in-water emulsions, micelles, mixed micelles and liposomes. An exemplary colloidal system for use as an in vitro and in vivo delivery vehicle is a liposome (e.g., an artificial membrane vesicle). In the case of non-viral delivery systems, an exemplary delivery vehicle is a liposome. The use of lipid formulations to introduce nucleic acids into host cells (in vitro, ex vivo or in vivo) is contemplated. In some embodiments, the nucleic acid is associated with a lipid. Nucleic acids associated with a lipid can be encapsulated within the aqueous interior of the liposome, dispersed within the lipid bilayer of the liposome, attached to the liposome via a linking molecule associated with the liposome and the oligonucleotide, entrapped in the liposome, complexed with the liposome, dispersed in a solution containing the lipid, mixed with the lipid, bound to the lipid, contained in the lipid as a suspension, contained or complexed with a micelle, or otherwise associated with the lipid. The lipid, lipid/DNA or lipid/expression vector associated composition is not limited to any particular structure in solution. For example, they may exist in bilayer structures, micelles, or "collapsed" structures. They may also be simply dispersed in solution, possibly forming aggregates of non-uniform size or shape. Lipids are fatty substances, which may be naturally occurring or synthetic lipids. For example, lipids include aliphatic droplets naturally occurring in the cytoplasm and a class of compounds containing long chain aliphatic hydrocarbons and derivatives thereof such as fatty acids, alcohols, amines, amino alcohols, and aldehydes.

Lipids suitable for use are available from commercial sources. For example, dimyristoyl phosphatidylcholine ("DMPC") is available from Sigma, st.louis, MO; dicetyl phosphate ("DCP") is available from K & K Laboratories (Plainview, N.Y.); cholesterol ("Choi") is available from Calbiochem-Behring; dimyristoyl phosphatidylglycerol ("DMPG") and other lipids are available from Avanti Polar Lipids, inc (Birmingham, AL.). A stock solution of lipids in chloroform or chloroform/methanol may be stored at about-20 ℃. Chloroform can be used as the only solvent because it evaporates more readily than methanol. "liposome" is a generic term that encompasses various unilamellar and multilamellar lipid vehicles formed by the production of a closed lipid bilayer or aggregate. Liposomes are characterized by a vesicle structure with a phospholipid bilayer membrane and an internal aqueous medium. Multilamellar liposomes have multiple lipid layers separated by an aqueous medium. Phospholipids spontaneously form when suspended in excess aqueous solution. The lipid components self-rearrange before forming a closed structure and entrap water and dissolved solutes between the lipid bilayers (Ghosh et al, glycobiology 5:505-510 (1991)). However, compositions having a structure in solution that is different from the normal vesicle structure are also contemplated. For example, lipids may be assumed to have a micelle structure or exist only as heterogeneous aggregates of lipid molecules. Lipofectamine-nucleic acid complexes are also contemplated.

Regardless of the method used to introduce the exogenous nucleic acid into the host cell, the presence of the recombinant nucleic acid sequence in the host cell can be routinely confirmed by a variety of assays known in the art. Such assays include, for example, "molecular biology" assays such as DNA and northern blotting, RT-PCR, and PCR; "biochemical" assays, such as detecting the presence or absence of a particular peptide, identify agents that fall within the scope of the present disclosure, for example, by immunological means (ELISA and western blot) or by the assays described herein.

Reporter genes are used to identify potentially transfected cells and to assess the functionality of regulatory sequences. In general, a reporter gene is a gene that is not present in or expressed by a recipient organism, tissue or cell and encodes a polypeptide whose expression is evidenced by some readily detectable property, such as enzymatic activity. The expression of the reporter gene is determined at a suitable time after introduction of the DNA into the recipient cell. Suitable reporter genes include, but are not limited to, genes encoding luciferases, beta-galactosidases, chloramphenicol acetyl transferase, secreted alkaline phosphatase, or green fluorescent protein genes (e.g., ui-Tei et al, FEBS Lett.479:79-82 (2000)). Suitable expression systems are known in the art and can be prepared or commercially available using known techniques. In general, constructs with minimal 5' flanking regions that show the highest expression levels of the reporter gene are identified as promoters. Such promoter regions may be routinely linked to reporter genes and used to assess the ability of an agent to modulate promoter-driven transcription.

Many selection systems are available for use in mammalian host-vector expression systems, including but not limited to the herpes simplex virus thymidine kinase, hypoxanthine-guanine phosphoribosyl transferase, and adenine phosphoribosyl transferase (Lowy et al, cell 22:817 (1980)) genes. In addition, antimetabolite resistance can be used as a basis for selection of, for example, dhfr, gpt, neo, hygro, trpB, hisD, ODC (ornithine decarboxylase) and glutamine synthase systems.

In some embodiments, the initiator N-terminal methionine is contained at the NH terminus of the ligand. In many cases, the isolated ligand has no N-terminal methionine residue, which is presumed to be cleaved during expression. In many cases, only a portion of the purified ligand contained an N-terminal methionine in the resulting mixture. It will be apparent to those skilled in the art that the presence or absence of an N-terminal methionine does not affect the functionality of the ligands and affinity agents described herein.

Ligand purification

Once the ligand or ligand fusion protein or multimer is produced by recombinant expression, it can be purified by recombinant protein purification methods known in the art, such as by chromatography (e.g., ion exchange chromatography, affinity chromatography, and size exclusion column chromatography), centrifugation, differential solubility, or by any other standard technique for purifying proteins. In some embodiments, the ligand is optionally fused to a heterologous polypeptide sequence specifically disclosed herein or known in the art to facilitate purification. In some embodiments, the ligands (e.g., antibodies and other affinity matrices) and optionally the ligands or other components of the ligand fusion composition bound by these ligands are removed from the composition prior to final preparation of the ligands using techniques known in the art.

Chemical synthesis of ligands

In addition to recombinant methods, ligand production can be performed using a variety of liquid and solid phase chemical methods known in the art, using organic chemical synthesis of the desired polypeptide. Various automated synthesizers are commercially available and can be used according to known protocols. See, for example, tam et al, j.am.chem.soc.,105:6442 (1983); merrifield, science,232:341-347 (1986); barany and Merrifield, the Peptides, gross and Meienhofer, editions, academic Press, new York,1-284; barany et al, int.j.pep.protein res.,30:705 739 (1987); kelley et al Genetic Engineering Principles and Methods, setlow, J.K., edit Plenum Press, NY.1990, vol 12, pages 1-19; stewart et al, solid-Phase Peptide Synthesis, W.H. Freeman Co., san Francisco,1989. One of the advantages of these methods is that they allow for the incorporation of unnatural amino acid residues into ligand sequences.

Ligands and multimers used in the methods of the present disclosure may be modified during or after synthesis or translation, e.g., by glycosylation, acetylation, benzylation, phosphorylation, amidation, pegylation, formylation, derivatization by known protecting/blocking groups, proteolytic cleavage, conjugation to antibody molecules, hydroxylation, iodination, methylation, myristoylation, oxidation, pegylation, proteolytic processing, phosphorylation, prenylation, racemization, selenoylation, sulfation, ubiquitination, etc. (see, e.g., crigton, proteins: structures and Molecular Properties, 2 nd edition (W.H. Freeman and Co., N.Y., 1992), postranslational Covalent Modification of Proteins, johnson, editions (Academic Press, new York, 1983), pages 1-12; seifer, meth. Enzymol.,182:626-646 (1990)), rattan, ann. NY Acad. Sci., 663:62 (1992)). In some embodiments, the peptide is acetylated at the N-terminus and/or amidated at the C-terminus.

Any of a number of chemical modifications may be made by known techniques including, but not limited to, acetylation, formylation, and the like. In addition, the derivative may contain one or more non-classical amino acids.

In some embodiments, cyclization or macrocyclization of the peptide backbone is achieved by formation of side chains to side chain linkages. Methods for achieving this are well known in the art and may involve natural and unnatural amino acids. Pathways include disulfide formation, lanthionine formation or thiol alkylation (e.g., michael addition), amidation between amino and carboxylic acid side chains, click chemistry (e.g., azide-alkyne condensation), peptide binding, ring closure metathesis, and use of enzymes.

Affinity agent for purification

In affinity chromatography-based purification, a target of interest (e.g., a protein or molecule) is selectively isolated according to its ability to specifically and reversibly bind to a ligand, which is typically covalently coupled to a chromatography matrix. For example, the affinity ligands of the present disclosure can be used as reagents for affinity purification of AAV8 or AAV8 variants from clarified cell culture broth (CCCF) or natural sources such as biological samples (e.g., serum).

In some embodiments, a ligand or multimer that specifically binds AAV8 or AAV8 variants is immobilized on a bead, such as an agarose bead, to form an affinity separation matrix, and then used to affinity purify the target.

Methods of covalently coupling proteins to surfaces are known to those skilled in the art, and peptide tags useful for attaching ligands to solid surfaces are known to those skilled in the art. In addition, the ligand may be attached (i.e., coupled, linked, or adhered) to the solid surface using any agent or technique known in the art. In some embodiments, the solid support comprises a bead, glass slide, chip, and/or gelatin. Thus, a range of ligands can be used to fabricate arrays on solid surfaces using techniques known in the art. For example, U.S. publication No. 2004/0009530, which is incorporated herein by reference, discloses a method for preparing an array.

In some embodiments, the ligand or multimer is used to isolate an AAV8 particle or capsid, or variant AAV8 particle or capsid, by affinity chromatography. In some embodiments, the ligand or polymer is immobilized on a solid support. The ligand or multimer can be immobilized on a solid support using other techniques and reagents described herein or known in the art. Suitable solid supports are described herein or are known in the art and are suitable for packing chromatography columns in particular embodiments. The affinity agent may be packed in columns of various sizes and run at various linear velocities, or the immobilized affinity ligand may be contacted with a solution under conditions conducive to the formation of a complex between the ligand and the AAV8 capsid or AAV8 variant capsid. Unbound material can be washed away. Suitable wash conditions can be readily determined by those skilled in the art. Examples of suitable washing conditions are described in Shukla and Hinckley, biotechnol prog.2008, 9 months to 10 months; 24 (5): 1115-21.Doi:10.1002/btpr.50.

In some embodiments, chromatography is performed by mixing solutions containing the target of interest and the ligand, and then isolating the complex of the target of interest and the ligand (e.g., AAV8 and ligand). For example, the ligand or multimer is immobilized on a solid support, such as a bead, and then separated from solution by filtration along with the AAV8 capsid or AAV8 variant capsid. In some embodiments, the ligand or multimer is a fusion protein containing a peptide tag, such as a polyHis tail or streptavidin binding region, that can be used to isolate the ligand or multimer after complex formation using an immobilized metal affinity chromatography resin or streptavidin coated substrate. Once isolated, the AAV8 capsid or AAV8 variant capsid can be released from the ligand or multimer under elution conditions and recovered in purified form.

In some embodiments, the ligands or multimers of the present disclosure are coupled to a highly crosslinked agarose base matrix that can be used in bioprocess applications. The attachment of the ligand or multimer to the base matrix can ensure ligand accessibility by flexible spacers and subsequently lead to high binding capacity. The affinity of the ligands and multimers of the present disclosure ensures highly specific binding of AAV8 at near neutral pH (pH 6-9) while being able to elute at a pH of up to 4.5. Furthermore, the ligands of the present disclosure are designed to enhance base stability, enabling the reuse of 0.5M NaOH in cleaning and sanitizing applications.

In another aspect, the present disclosure provides a method of isolating an AAV8 particle or capsid and/or an AAV8 variant particle or capsid, wherein the separation matrix as disclosed above is used. In certain embodiments, the method comprises the steps of: (a) contacting a liquid sample comprising AAV8 particles and/or capsids and/or AAV8 variant particles and/or capsids with a separation matrix as disclosed above, (b) washing the separation matrix with a wash solution, (c) eluting AAV8 and/or AAV8 variant particles and/or capsids from the separation matrix with an elution solution, and (d) washing the separation matrix with a wash solution, which may also be referred to as a Cleaning In Place (CIP) solution, e.g. for a contact (incubation) time of at least one minute, e.g. one to four minutes or more.

Suitable compositions of liquid samples, washes and eluents, as well as the general conditions under which separation is performed, are well known in the art of affinity chromatography. For example, a liquid sample comprising AAV8 and/or AAV8 variant particles and/or capsids may comprise Host Cell Proteins (HCPs), such as HEK293T cells. The host cell protein may be desorbed during step (b).

AAV8 binding has been demonstrated in buffers that approach neutral pH (6-9) and have a wide range of ionic strengths (e.g., 100-400mM NaCl). Conventional buffers, such as phosphate, citrate, acetate, tris, may be used for equilibration and loading.

In some embodiments, the solution or sample containing AAV8 particles or capsids and/or AAV8 variant particles or capsids (i.e., viral particles/capsids) is concentrated, e.g., by ultrafiltration, prior to contacting the solution with the separation matrix. For example, a solution containing viral particles/capsids, such as clarified cell culture material, may be concentrated up to 20-fold. Concentration of the viral particles/capsids reduces the loading time of affinity chromatography. Due to thermodynamic equilibrium effects, an increase in concentration may also positively influence the binding capacity, which may lead to a reduction in the volume of separation matrix required for purification. Concentrating the virus/capsid solution also enables a significant reduction in processing time.

Alternatively, the solution or sample containing AAV8 particles or capsids and/or AAV8 variant particles or capsids is a non-concentrated or diluted solution, such as clear cell culture media (CCCF). As shown in fig. 4, the affinity separation matrix of the present disclosure is characterized by the ability to process CCCF at high volumetric flow rates, thereby enabling capture from dilute CCCF streams.

Elution of the viral particles and capsids is typically achieved by lowering the pH (e.g. 2.0-3.0), but higher pH values may also be used. The optimal conditions for eluting AAV8 and variants thereof can be readily determined by those skilled in the art.

The affinity agents of the present disclosure are alkali resistant and can be cleaned using NaOH at concentrations up to 0.5M. In certain embodiments, a CIP regimen, for example, of up to 30 to 60 minutes of exposure to 0.5M NaOH per cycle, can ensure chromatographic performance uniformity over several cycles (e.g., 15-30 cycles), including up to 70% -90% initial AAV8 binding capacity and low residual DNA and HCP levels, as well as substantially unchanged flow capacity.

Examples

Example 1

Peptides were synthesized by standard Fmoc solid phase peptide synthesis techniques and purified by preparative reverse phase UPLC. The purity of the peptides was assessed by RP HPLC with uv and quadrupole time-of-flight mass spectrometry detection.

Recombinant protein ligands are expressed in E.coli and/or Pichia using standard techniques. The ligand was purified using multi-column chromatography. For his-tagged ligands, IMAC was used as the primary capture step. Using Avitag ^TM The system (Avidity, aurora, CO) produces biotinylated ligands. Preparation of the Avitag-bearing by omitting exogenous Biotin ^TM Non-biotinylated ligands of the sequences. The purity and identity of the recombinant protein ligand was assessed by a combination of SDS-PAGE, RP UPLC, quadrupole time-of-flight mass spectrometry and SEC (Sephadex S75, cytiva, marlborough, mass.). In many cases, the isolated ligand has no N-terminal methionine residue, which is presumed to be cleaved during expression. In many cases Next, only a part of the purified ligand contained N-terminal methionine in the obtained mixture. The presence or absence of N-terminal methionine does not affect the binding specificity or other properties of the ligand.

Example 2

This example demonstrates the binding of biotinylated ligand to AAV8 capsids using biolayer interferometry (ForteBio, menlo Park, ca.). Biotinylated ligand was immobilized on the sensor and incubated with a solution (pH 7.0) containing 5X 1011vp/mL in 100mM sodium phosphate, 100mM sodium chloride, 0.01% (w/v) bovine serum albumin and 0.1% (v/v) Triton X-100. Blank sensor and non-binding sequence (SEQ ID No. 54) were included as controls. The association phase shows an initial linear increase in response, which is a typical feature of AAV. As the sensor becomes saturated, the sensor map shows a greater curvature. FIG. 1 shows an example of ligand SEQ ID No. 14. Responses were measured after 4000 seconds incubation time and are listed below.

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Example 3

This example demonstrates the sodium hydroxide stability of the affinity ligand. The ligand was incubated in 0.5M NaOH for 16 hours and then neutralized. The binding of NaOH-treated ligand was measured and compared to untreated ligand as described in example 1. The retained binding is calculated according to the following formula:

Binding = (measured response after NaOH treatment)/(measured response without treatment) ×100% retention

The data is shown in fig. 2, which demonstrates that many affinity ligands of the present disclosure exhibit high stability under the test conditions.

Example 4

This example demonstrates the use of an affinity agent comprising an affinity ligand as described herein for affinity purification of AAV8 particles. Clarified cell culture feed stream (CCCF) containing AAV8 viral capsids at titers of about 8E12 total capsids/mL was used. The 0.3cm ID x 5cm column was operated as shown in the following table. The resin comprises ligand density of 1.9-2.0mg/mL.

Table 1.

Eluted material was analyzed by SDS-PAGE together with the fractions stripped. The data are shown in fig. 3. Radiographs show that the affinity resin comprising an affinity ligand with the amino acid sequence SEQ ID NO.53 allows for high yields and purity of AAV8 capsids in the eluate.

Example 5

This example demonstrates that the affinity agents of the present disclosure enable mild elution conditions. A3 mm ID x 25mm column packed with resin containing ligand SEQ ID NO.14 was challenged with about 3.5E14vp/mL of resin and eluted with pH 4 buffer containing 1, 6-hexanediol or propylene glycol. The results shown in the table below demonstrate that the use of these additives enables elution at higher pH. Hexanediol provided higher yields and better purity in this experiment. HCP = host cell protein.

Table 2.

Additive agent	20% of 1, 6-hexanediol	70% propylene glycol
			Yield (vp/mL resin)	2.9E14	1.5E14
HCP(ppm)	1900	3800
			DNA(ppm)	540	430

Example 6

This example demonstrates the high binding capacity of the disclosed affinity agent and demonstrates that the high binding capacity is maintained at a faster flow rate (i.e., shorter residence time).

An affinity agent comprising an affinity ligand corresponding to SEQ ID No.53 bound to a resin was packed into a 3mm x 50mm column, which was challenged with purified AAV8 capsids. The penetration curves shown in fig. 4 were obtained at residence times of 1, 2, 3 and 4 minutes. The capsids in the effluent were measured by capsid ELISA. The high capacity combination of short residence times results in very high productivity enabling purification of AAV8 capsids using affinity agents at various process configurations and scales.

The above examples demonstrate that the affinity resins of the present disclosure can be fine tuned to achieve different performance characteristics that may be required for different applications. Many modifications and other embodiments of the disclosure set forth herein will come to mind to one skilled in the art to which these disclosure pertains having the benefit of the teachings presented in the foregoing descriptions and the associated drawings. Therefore, it is to be understood that the disclosure is not to be limited to the specific embodiments disclosed and that modifications and other embodiments are intended to be included within the scope of the appended claims and list of embodiments disclosed herein. Although specific terms are employed herein, they are used in a generic and descriptive sense only and not for purposes of limitation.

Any of the methods disclosed herein need not be performed in the order recited. The methods disclosed herein include certain actions taken by a practitioner; however, they may also include any third party indication of such behavior, whether explicit or implicit.

TABLE 3 sequence

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Claims

1. An affinity ligand comprising an amino acid sequence represented by the following formula, from the N-terminus to the C-terminus,

wherein the method comprises the steps of

(a) [ A ] comprises a first alpha-helix forming peptide domain;

(b)X ₁ a, R, N, S, D, L, Q or I, preferably R;

(c)X ₂ g, H, P or S, preferably S;

(d)X ₃ is A or Y, preferably Y;

(e)X ₄ is R or S, preferably R;

(f)X ₅ e, H or Q, preferably Q;

(g)X ₆ is E or S, preferably S;

(h)X ₇ f, V or Y, preferably F;

(i)X ₈ a, E or R, preferably a;

(j)X ₉ h, I or N, preferably H;

(k)X ₁₀ a, E or R, preferably a;

(1)X ₁₁ is D or E, preferably D;

(m)X ₁₂ is K or R, preferably K;

(n)X ₁₃ q, T or Y, preferably Y;

(o)X ₁₄ d, L or R, preferably R;

(p)X ₁₅ is A or N, preferably N;

(q)X ₁₆ d, L or R, preferably R;

(r)X ₁₇ a, D, E, F, G, I, K, L, P, Q, R, S, T or Y, preferably I;

(s)[B]comprises an amino acid sequence QAPX ₁₈ (SEQ ID NO: 2) or QAPX ₁₈ Peptide of VD (SEQ ID NO: 3), wherein X ₁₈ A, K or R; and is also provided with

Wherein the affinity ligand specifically interacts with an adeno-associated virus subtype 8 (AAV 8) particle or capsid or a variant particle or capsid of AAV 8.

2. The affinity agent of claim 1, wherein [ a ] comprises a polypeptide having the amino acid sequence of SEQ ID NO: 4.

3. The affinity agent of claim 1, wherein [ a ] comprises a polypeptide having the amino acid sequence of SEQ ID NO: 5.

4. Affinity ligand according to claim 1 or 2, wherein [ A ] is N-terminal to M or MAQGT (SEQ ID NO: 6).

5. The affinity ligand according to any one of claims 1-4, wherein [ B ] has the amino acid sequence QAPKVD (SEQ ID NO: 7) or QAPRVD (SEQ ID NO: 8).

6. The affinity ligand according to any one of claims 1-4, wherein [ B]Comprises a polypeptide having the amino acid sequence QAPX ₁₈ -[C]The peptide of (SEQ ID NO: 9), wherein [ C ]]Is a peptide domain selected from the group consisting of:

(a)VDGQAGQGGGSGLNDIFEAQKIEWHEHHHHHH(SEQ ID NO：10)，

(b)GQAGQGGGSGLNDIFEAQKIEWHEHHHHHH(SEQ ID NO：11)，

(c) VDGLNDIFEAQKIEWHEHHHHHH (SEQ ID NO: 12) and

(d)GLNDIFEAQKIEWHEHHHHHH(SEQ ID NO：13)。

7. the affinity ligand of any one of claims 1-6, further comprising a C-terminal cysteine or lysine.

8. The affinity ligand of any one of claims 1-7, wherein said ligand comprises the amino acid sequence of SEQ ID No: 14-93.

9. The affinity ligand of claim 8, wherein said ligand comprises the amino acid sequence of SEQ ID NO:14 or SEQ ID NO:53.

10. the affinity ligand of any one of claims 1-9, wherein the ligand further comprises at least one heterologous agent operably linked to the affinity ligand to form a conjugate

11. The affinity ligand of claim 10, wherein the heterologous agent is selected from the group consisting of: one or more small molecule diagnostic or therapeutic agents; DNA, RNA, or hybrid DNA-RNA molecules; a trackable marker; a radioactive agent; an antibody; a single chain variable domain; and immunoglobulin fragments.

12. A multimer comprising a plurality of affinity ligands according to any one of claims 1 to 11.

13. The multimer of claim 12, which is a dimer, trimer, tetramer, pentamer, hexamer, heptamer, octamer, or nonamer.

14. A nucleic acid or vector encoding an affinity ligand according to any one of claims 1-9 or a multimer according to claim 12 or 13.

15. A separation matrix comprising at least one affinity ligand according to any one of claims 1-9 or at least one multimer according to claim 12 or 13.

16. The separation matrix of claim 15, wherein a plurality of affinity ligands of any one of claims 1-9 or a multimer of claim 12 or 13 is coupled to a solid support.

17. The separation matrix of claim 16, wherein the affinity ligand or multimer is coupled to the solid support via a urethane linkage.

18. The separation matrix of any one of claims 15-17, wherein the solid support is a chromatography resin or matrix.

19. The separation matrix of claim 18, wherein the solid support is a cross-linked agarose matrix.

20. A method of isolating an adeno-associated virus subtype 8 (AAV 8) particle or capsid, comprising contacting the AAV8 particle or capsid with the separation matrix of any one of claims 15-19.

21. The method of claim 20, comprising the steps of: (a) contacting a liquid sample comprising AAV8 particles or capsids with the separation matrix, (b) washing the separation matrix with a wash solution, (c) eluting the AAV8 particles or capsids from the separation matrix with an elution solution, and (d) washing the separation matrix with a wash solution.

22. The method of claim 21, wherein the cleaning solution comprises 0.1-0.5M NaOH.

23. The method of claim 21 or 22, wherein steps (a) - (d) are repeated at least 10 times.

24. An expression system comprising the nucleic acid or vector of claim 14.